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Yorodumi- PDB-1p16: Structure of an mRNA capping enzyme bound to the phosphorylated c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p16 | ||||||
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Title | Structure of an mRNA capping enzyme bound to the phosphorylated carboxyl-terminal domain of RNA polymerase II | ||||||
Components |
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Keywords | TRANSFERASE / GUANYLYLTRANSFERASE / CANDIDA ALBICANS / RNA POLYMERASE II / TRANSCRIPTION / CAPPING / CTD / MRNA | ||||||
Function / homology | Function and homology information mRNA capping enzyme complex / 7-methylguanosine mRNA capping / mRNA guanylyltransferase activity / mRNA guanylyltransferase / GTP binding Similarity search - Function | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | ||||||
Authors | Fabrega, C. / Shen, V. / Shuman, S. / Lima, C.D. | ||||||
Citation | Journal: Mol.Cell / Year: 2003 Title: Structure of an mRNA capping enzyme bound to the phosphorylated carboxy-terminal domain of RNA polymerase II. Authors: Fabrega, C. / Shen, V. / Shuman, S. / Lima, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p16.cif.gz | 182.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p16.ent.gz | 150.8 KB | Display | PDB format |
PDBx/mmJSON format | 1p16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/1p16 ftp://data.pdbj.org/pub/pdb/validation_reports/p1/1p16 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 46496.660 Da / Num. of mol.: 2 / Fragment: residues 1-395 od SWS P78587 / Mutation: I2V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Description: modified pet15b (N-terminal SUMO fusion) / Gene: CGT1 / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Variant (production host): B834 (DE3) / References: UniProt: P78587, mRNA guanylyltransferase #2: Protein/peptide | Mass: 2417.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: NATURALLY OCCURING REPETITIVE YSPTSPS SEQUENCE |
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-Non-polymers , 4 types, 438 molecules
#3: Chemical | #4: Chemical | ChemComp-G / | #5: Chemical | ChemComp-GTP / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.13 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 3M ammonium phosphate, 50mM hepes, 3% DMSO, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.9792 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 15, 2001 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. all: 30976 / Num. obs: 30976 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.8 / % possible all: 89.9 |
Reflection | *PLUS Highest resolution: 2.7 Å / Num. obs: 56988 / Num. measured all: 495195 |
Reflection shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / % possible obs: 89.9 % |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→19.7 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1505758.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.1852 Å2 / ksol: 0.3069 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→19.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 20 Å / Num. reflection obs: 26585 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.7 Å / Rfactor Rfree: 0.336 |